Get them growing! A public catalog of cultured bacterial strains from the mouse intestine

Ask children what they want to do in their future; none of them would answer “become a passionate collector of bacteria”. But this is what I like to do! Hunting these microscopic organisms is fun, even in the dark matter of our gut.

Go to the profile of Thomas Clavel
Aug 15, 2016
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Bacteria colonizing the intestine of mammals influence host physiology and the onset and maintenance of diseases. This is nowadays textbook knowledge thanks to intensive research in the field of gut microbial ecology and microbe-host interactions, with a particular rebound of interest in the last fifteen years primarily due to breakthrough in sequencing technologies. However, the resolution of these molecular techniques is utterly dependent on the quality of databases used to interpret datasets. This is where cultivating bacteria is valuable: it allows discovery of novel taxa and eventually the implementation of databases if detailed genetic work is performed.

Mice are the most widely used animals in research. In the field of microbe-host interactions, germfree mice (i.e. mice that live in a sterile environment and can be colonized with microorganisms of choice) are particularly useful, for instance to assess the effects of colonization on the development of diseases. Moreover, intestinal colonization can be host-specific (the occurrence of specific bacteria is different between human and mice for instance). The problem is that little information has been available on the diversity and identity of bacterial species in the mouse gut: many of the sequences obtained by molecular studies cannot be annotated, and reference bacterial strains have not been available.

Ten years ago, when I was hired at TU Munich as microbiologist in a lab dealing mostly with immunology, I started doing what I could do best: isolating and identifying bacteria using intestinal samples from some of the mouse models widely used around me. I focused primarily on anaerobic bacteria, which cannot grow in normal air and have to be handled in chambers with an inner atmosphere deprived of oxygen.

An anaerobic chamber for growing fastidious bacterial species from the intestine.

Isolating gut bacteria is fascinating. You are always full of hopes when designing new experimental conditions, the ones that may eventually get you to the species you have been looking for. And it is always very exciting to look at these little cells under the microscope, see how they look like, and eventually get a glimpse of what they are and possibly what they can do by sequencing their genomes or some specific phylogenetic marker genes. It can be frustrating too though: when you obtain for the thousandth time usual suspects such as Escherichia coli or lactobacilli; it can be time consuming (several weeks or even months can be necessary to subculture fastidious anaerobes and make sure that cultures are pure); and most of all, it used not to be very much rewarding to isolate and describe bacteria in the current molecular era of microbial ecology.

Over the years isolating and describing bacteria, we have realized that the community of scientists would greatly benefit from a common resource cataloging mouse gut bacterial strains and making them available for research purposes. Things put into place slowly. The pool of strains we obtained was growing. The field was ready to acknowledge that culture methods had been neglected over the last decades. Involvement of the internationally recognized bioresource DSMZ (German Collection of Microorganisms and Cell Cultures) was a key element in the project. Indeed, isolating bacteria from the mouse intestine was carried out in the 1970’s already, but strains got lost over the years. Hence, besides providing novel bacterial diversity, functionality, and host-specificity of gut colonization, the major goal we followed was to help as many researchers as possible by establishing a public resource. The mouse intestinal Bacterial Collection (miBC) was born, and it will hopefully be useful to many ( Anybody who, like us, has fun isolating microorganisms from the mouse intestine and wants to contribute to the extension of this unique resource is welcome to get in touch with us.

Thomas Clavel, PhD

Technical University of Munich, ZIEL Institute for Food and Health, Germany


Go to the profile of Thomas Clavel

Thomas Clavel

Senior scientist at TUM, TUM

I am a microbiologist with 14 years experience in gut microbiota research. My primary interests are the study of bacterial diversity, the description of novel bacterial taxa, and the interactions between gut commensals and their environment. My main research activities are focused on culture- and sequence-based analysis of microbiomes, and the characterization of single strains for use in minimal communities.


Go to the profile of Ben Johnson
Ben Johnson over 1 year ago

Really interesting post - and a great open resource for microbiologists.

The article in Nature Microbiology that describes the Mouse Intestinal Bacterial Collection (miBC) is published, open access, here: